smrnaseq

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Version `2.14.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...

nf-core-bot

### Description of the bug I'm wondering if the `protocol` option is well interpreted for the adapter trimming. If I use `--protocol illumina` or `--protocol qiaseq`, there is no difference...

nservant

HTTP 404 NOT FOUND for channel conda-base <https://conda.anaconda.org/conda-base>

9

### Description of the bug Hi! I've been trying to run the latest version of this pipeline: 2.3.1 using conda and I encountered this error: ``` ERROR ~ Error executing...

karlaarz

Valid `--mirtrace_species` is required even with `--mirgenedb` when `--mirgenedb_species` is given

4

### Description of the bug According to the documentation, it appears that the miRNA databases miRBase (used by default) and MirGeneDB are alternative sources of reference files, and either can...

tdanhorn

--mirna_gtf for organism with no miRBase GFF file

4

### Description of the bug I'm using sheep miRNA data. miRBase contains a few entries for sheep miRNAs but does not provide a gff file on it's download page. I...

OliverH96

Concatenate technical repeats

1

### Description of feature When running smrnaseq with technical repeats I get the error: ``` Process `NFCORE_SMRNASEQ:SMRNASEQ:MIRNA_QUANT:MIRTOP_QUANT` input file name collision -- There are multiple input files for each of...

ojziff

### Description of feature At the moment, we auto-detect adapter sequence in each sample independently. This allows us to accomodate runs that are a mixture of different adapters. If we...

robsyme

INDEX_GENOME: Bowtie build error

4

### Description of the bug Error in the genome index step using both 2.3.0 or dev versions using the command below. All reference files are from mirbase and fasta from...

AhmedMohamed1993

bcbio-nextgen error for paired end data

3

### Description of the bug The bug occurs due to unrecognized arguments passed to the `seqcluster` command. It expects input files in a specific format but receives unexpected arguments, causing...

vishal7245

Error in DGEList(counts = data, genes = rownames(data)) : non-numeric values found in counts

2

### Description of the bug This issue is identical to #218, which was closed but not resolved. After debugging, the problem is that the `data` object being supplied to `DGEList(counts=data,genes=rownames(data))`...

mdozmorov